A key objective of this project is to simplify collaboration between the phylogeny and protein structure communities via the provision of easy to use tools for complex methods. We will achieve this by adding significant new functions to three popular Java-based applications that span phylogenetics on DNA (TOPALi) protein sequence analysis and prediction (JalView) and visualisation of three-dimensional structure (AstexViewer@MSD-EBI ) vs
Collaboration Université de Dundee (bbsrc – the Biotechnology and Biological Sciences Research Council) - Biomathematics & Statistics Scotland (BioSS) Jalview is a multiple alignment editor TOPALi provides an intuitive graphical interface for working with existing statistical methods designed for detecting recombination in DNA sequence alignments. AstexViewer@EBI structural data browser a version of the Astex Viewertm for molecular structure developed by the EBI's Macomolecular Structure Database group, and TOPAli – a tool for phylogenetic and recombination analysis which is developed at the Scottish Crop Research Institute. Topali detect the position of recombinaison breakpoints within DNA multiple alignments
Visualisation & Analysis of Biological Sequences, Alignments & Structures The aim of this project is to simplify collaboration between the phylogeny and protein structure communities via the provision of easy to use tools for complex methods. A significant part of this challenge is to make independent tools interact together by transparent data exchange. by adding SOAP support, and significant new functions to three popular Java-based applications that span phylogenetics on DNA (TOPALi) protein sequence analysis and prediction (JalView) and visualisation of three-dimensional structure (AstexViewer™@EBI-MSD (AV@EBI-MSD)). Each of these programs has a wide userbase (Jalview has over 25,000 google hits), and analytical tools essential to integrative biology. Projet qui a commencé October 2004 3 outils Topali JalView And AstexViewer@EBI développé au sein de l’ebi et dont je suis chargé de son intégration
Sequences sets Alignements Annotations historique Phylogenic tree (global tree of species)
2 applications Av is owned by astex technology Lightweight AV Client and browser compatibility (Java 1.1)
Rotation translation matrix -> SSM
The "Structure integration with function, taxonomy and sequence (SIFTS) initiative" aims to work towards the integration of various bioinformatics resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt , which are primary archival databases for structure and sequence data, is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. The project was started in the year 2001 and has resulted in creating a robust mechanisms for exchanging data between the two primary data resources. This has dramatically improved the quality of annotation in both databases and is aiding the continuing improvements of legacy data. In the longer term this project will allow for not only the better and closer integration of derived-data resources but will continue to improve the quality of all data in the primary resources.
Avoid duplicated files Clusta
Omega torion angle The "Structure integration with function, taxonomy and sequence (SIFTS) initiative" aims to work towards the integration of various bioinformatics resources. One of the major obstacles to the improved integration of structural databases such as MSD and sequence databases like UniProt , which are primary archival databases for structure and sequence data, is the absence of up to date and well-maintained mapping between corresponding entries. We have worked closely with the UniProt group at the EBI to clean up the taxonomy and sequence cross-reference information in the MSD and UniProt databases. The project was started in the year 2001 and has resulted in creating a robust mechanisms for exchanging data between the two primary data resources. This has dramatically improved the quality of annotation in both databases and is aiding the continuing improvements of legacy data. In the longer term this project will allow for not only the better and closer integration of derived-data resources but will continue to improve the quality of all data in the primary resources.
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